Exporting from blender to unity
There are a couple ways around this:


Split your .blend files: This is probably the best thing to do anyway, since you seem to be using Unity's automagic importer.  This will allow Unity to conceptually separate your meshes into their own discreet thing, and if you change them, the changes will propagate correctly.
Split through prefab:  You can take the multi-tree model, delete all the meshes down to one tree, and save those changes as a separate prefab.  This has issues though, mostly because if the file change noticeably, you will need to redo the prefab.  


Scale is mostly arbitrary, but you can change Unity's import scale by clicking the model in the assets browser, then going to the inspector and playing with the Scale Factor (top line).